The Senegal international broke the deadlock in the 51st minute of the game after receiving a pass from Matteo Politano.
Then in the 76th minute, Hamed Junior Traore leveled for Aurelio Andreazzoli’s men following Salih Ucan’s assist.
With nine minutes to time, Radja Nainggolan scored the match-winning goal to help his side end the season on a winning note.
Having been cautioned earlier, Balde saw his second yellow card and was subsequently sent off in added time.
The victory ensured that Inter ended the season with a Champions League ticket after finishing fourth on the table with 69 points from 38 games.
Balde ended his debut campaign with Inter with five goals in 28 appearances across all competitions.